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- PDB-6smc: mouse Interleukin-12 subunit beta - p80 homodimer in space group P1 -

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Basic information

Entry
Database: PDB / ID: 6smc
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group P1
ComponentsInterleukin-12 subunit beta
KeywordsCYTOKINE / homodimer / antagonist / fibronectin / secreted glycoprotein
Function / homology
Function and homology information


Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / natural killer cell activation / T-helper cell differentiation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of natural killer cell proliferation / cytokine receptor activity / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / defense response to protozoan / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / negative regulation of protein secretion / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / positive regulation of defense response to virus by host / positive regulation of interleukin-12 production / : / cytokine activity / endosome lumen / negative regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to type II interferon / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / defense response to virus / cellular response to lipopolysaccharide / cell population proliferation / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. ...Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-12 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders12S0519N Belgium
Research Foundation - FlandersG0B4918N Belgium
Research Foundation - FlandersG0E1516N Belgium
CitationJournal: To Be Published
Title: Around she goes: the structure of mouse Interleukin-12 p80
Authors: Bloch, Y. / Savvides, S.N.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Experimental preparation / Category: database_2 / exptl_crystal_grow
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pdbx_details
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-12 subunit beta
B: Interleukin-12 subunit beta
C: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,66010
Polymers157,5944
Non-polymers3,0666
Water00
1
A: Interleukin-12 subunit beta
C: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3305
Polymers78,7972
Non-polymers1,5333
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint8 kcal/mol
Surface area34090 Å2
MethodPISA
2
B: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3305
Polymers78,7972
Non-polymers1,5333
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint11 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.074, 96.791, 107.780
Angle α, β, γ (deg.)68.586, 76.842, 85.827
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGVALVAL(chain 'A' and (resid 23 through 92 or (resid 95...AA65 - 6865 - 68
12LEULEULEULEU(chain 'A' and (resid 23 through 92 or (resid 95...AA8383
13LYSLYSASNASN(chain 'A' and (resid 23 through 92 or (resid 95...AA217 - 220217 - 220
24ARGARGVALVAL(chain 'B' and (resid 23 through 92 or (resid 95...BB65 - 6865 - 68
25LEULEULEULEU(chain 'B' and (resid 23 through 92 or (resid 95...BB8383
26LYSLYSASNASN(chain 'B' and (resid 23 through 92 or (resid 95...BB217 - 220217 - 220
37ARGARGVALVAL(chain 'C' and (resid 23 through 92 or (resid 95...CC65 - 6865 - 68
38LEULEULEULEU(chain 'C' and (resid 23 through 92 or (resid 95...CC8383
39LYSLYSASNASN(chain 'C' and (resid 23 through 92 or (resid 95...CC217 - 220217 - 220
410ARGARGVALVAL(chain 'D' and (resid 23 through 120 or (resid 121...DD65 - 6865 - 68
411LEULEULEULEU(chain 'D' and (resid 23 through 120 or (resid 121...DD8383
412LYSLYSASNASN(chain 'D' and (resid 23 through 120 or (resid 121...DD217 - 220217 - 220

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Components

#1: Protein
Interleukin-12 subunit beta / IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40


Mass: 39398.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues 1:22 form the signal peptide and should be cotranslationally cleaved.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S GlycoDelete / Production host: Homo sapiens (human) / References: UniProt: P43432
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 200 MM NAFORMATE, 100 MM NAPO4 PH 6.2, 10 % GLYCEROL, 20% MEDIUM PEG SMEAR (BCS CONDITION 40)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.5→48.76 Å / Num. obs: 21609 / % possible obs: 92.9 % / Redundancy: 4.12 % / Biso Wilson estimate: 119.7 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.233 / Net I/σ(I): 5.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
10.28-48.764.0523.468210.9960.05889.6
7.35-10.284.1516.515510.9970.07597.1
6.02-7.354.29.4619540.9880.14995.6
5.23-6.024.026.9322820.9880.19193.9
4.68-5.234.115.6924380.9840.23590.1
4.28-4.684.144.0627770.9510.36891.6
3.96-4.284.182.4630560.8920.62392.4
3.71-3.964.171.2832850.7291.117394
3.5-3.714.090.7734450.5781.85291.9

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.16_3549refinement
XDS20190315data reduction
XDS20190315data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SFF

6sff


Resolution: 3.5→48.76 Å / SU ML: 0.5686 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.1363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3098 2153 10.03 %
Rwork0.2787 19316 -
obs0.2818 21469 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.31 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9582 0 202 0 9784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210005
X-RAY DIFFRACTIONf_angle_d0.682213568
X-RAY DIFFRACTIONf_chiral_restr0.04481521
X-RAY DIFFRACTIONf_plane_restr0.00491719
X-RAY DIFFRACTIONf_dihedral_angle_d2.55286032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.580.38911460.42841218X-RAY DIFFRACTION86.17
3.58-3.670.40981450.40071260X-RAY DIFFRACTION95.38
3.67-3.770.41181570.42111332X-RAY DIFFRACTION95.76
3.77-3.880.40981240.39941344X-RAY DIFFRACTION93.15
3.88-4.010.39661610.35451264X-RAY DIFFRACTION93.63
4.01-4.150.32111370.32221326X-RAY DIFFRACTION93.42
4.15-4.320.32891290.28981249X-RAY DIFFRACTION91.56
4.32-4.510.35081490.31271285X-RAY DIFFRACTION92.16
4.51-4.750.30851330.27841250X-RAY DIFFRACTION90.87
4.75-5.050.31251410.24921242X-RAY DIFFRACTION89.51
5.05-5.440.28611360.24911270X-RAY DIFFRACTION91.06
5.44-5.980.2931490.26571314X-RAY DIFFRACTION94.88
5.98-6.850.29831490.27241326X-RAY DIFFRACTION95.84
6.85-8.620.29921510.24711354X-RAY DIFFRACTION97.1
8.62-48.760.2331460.19911282X-RAY DIFFRACTION92.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.479393458733.45403354322.318054382055.205548766691.818869284493.330057795660.1118336357010.29915242327-0.0836508728087-0.100784403135-0.00428229736590.5219575284660.368987134933-0.0796702069744-0.03866033535541.16675796598-0.129260800057-0.283952880340.7770735697570.2679841052351.3018279510351.0950418137-19.784475863654.9220226324
24.311855996721.797041221410.976078831993.692152229861.181548983072.97518786095-0.0302493030088-0.1913435191040.2411416881050.2009199103190.0290213252502-0.0443983156542-0.301841415860.3363558342910.0180131209410.994900365224-0.0333563965747-0.324750516740.6519607969420.2165032193471.18073285108-18.78525107196.56686254495-25.2151075872
33.247930389920.4211653224733.121938708231.278740611030.8129531235946.85987325963-0.02433430964570.54786069694-0.165654904406-0.2896861667440.1845299471170.533329320468-0.0586335314384-0.270125772054-0.1742796701381.35459906966-0.172641697652-0.5213323497390.928755540350.2302393447151.625673927148.265417694726.135129298332.2198151371
44.103758627210.2427280615651.159136613381.0058995251-0.01014905672121.198684525480.17728648732-0.318017908725-0.4983176190870.51831525810.0553039890163-0.3296220242790.2678460737360.192696085273-0.2028451466721.75639314176-0.183885642455-0.6489942737061.155279211710.3626711110031.5847588293-20.8083025313-35.97742876622.34432234636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

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